BN1567 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 3.9360e-07 3.6082e-05
Layer 2 4.0393e-06 1.0989e-03
Layer 4 7.4060e-06 2.9795e-05
Layer 5 2.5838e-05 1.8319e-04
Layer 6 2.5195e-04 1.4344e-02
WM 6.6613e-01 4.4970e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
INPP5F Expression Distribution
Gene Specificity Score (GSS)
INPP5F GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
INPP5F Layer 4 3.6289 0.8478
CPLX1 Layer 4 3.3281 0.8443
CABP1 Layer 4 3.3223 0.8437
GABRA1 Layer 4 3.4980 0.8376
CALY Layer 4 3.1602 0.8359
GNG3 Layer 4 2.9414 0.8346
MEF2C Layer 4 3.2715 0.8341
RIMS3 Layer 4 3.6211 0.8322
ATP6V0E2 Layer 4 2.7188 0.8321
SCN1B Layer 3 3.9756 0.8313
SERPINI1 Layer 4 3.0117 0.8298
ATP2B2 Layer 4 3.5586 0.8296
NEFM Layer 3 3.5137 0.8294
NCDN Layer 4 3.0781 0.8290
RGS4 Layer 5 3.0312 0.8288
TUBB4B Layer 4 3.0117 0.8287
ATP6V0A1 Layer 4 2.8281 0.8273
ATP1A1 Layer 4 2.9414 0.8268
PNMA2 Layer 4 2.9160 0.8256
DCLK1 Layer 5 3.1328 0.8241
ATP2A2 Layer 3 2.8711 0.8233
ATP5MC3 Layer 4 2.7656 0.8225
ATP6V1B2 Layer 4 2.9805 0.8224
VGF Layer 4 3.8301 0.8224
EVL Layer 4 3.1055 0.8222
BEX5 Layer 4 3.1797 0.8221
TTC9B Layer 4 3.0996 0.8214
CEND1 Layer 4 3.0645 0.8210
PGK1 Layer 4 2.8711 0.8209
SCAMP5 Layer 4 3.0059 0.8208
NDRG3 Layer 4 3.0586 0.8206
DIRAS1 Layer 4 3.4531 0.8203
NEDD8 Layer 3 2.6367 0.8202
NPTN Layer 4 3.1797 0.8200
MYO5A Layer 4 3.1875 0.8198
CTNNA2 Layer 4 2.8906 0.8196
MOAP1 Layer 4 3.0586 0.8196
SLC25A5 Layer 3 2.7012 0.8195
ATP5F1D Layer 4 2.6543 0.8193
TUBB3 Layer 4 3.3223 0.8191
SPOCK2 Layer 4 2.8086 0.8188
REEP2 Layer 4 2.7656 0.8184
STXBP1 Layer 4 2.9414 0.8177
WSB2 Layer 4 2.9082 0.8176
BEX2 Layer 4 2.7598 0.8175
BMERB1 Layer 4 3.1523 0.8174
SYNGR1 Layer 4 3.0449 0.8173
STX1B Layer 4 2.8711 0.8170
TMOD2 Layer 4 3.1113 0.8164
FAIM2 Layer 4 2.7129 0.8163

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1567
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1567_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1567/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1567/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1567/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1567/report/PD/BN1567_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1567/report/PD/BN1567_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 05:11:15
  • Number of Processes: 10
  • Spending Time: 0h 2m